title: R2_D09_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R2_D09_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

status: Public on Nov 26 2019

type: SRA

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

country: USA

institute: UC Davis

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_root_Pool1_LnRep1.fq.gz

library_source: transcriptomic

data_processing:
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference transcriptome of S. lycopersicum (v3.2) using bowtie with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: ITAG3.2 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: comma separated files (one for RNA-Seq another for TRAP-Seq data) with raw counts for each sample (RNASeq tech reps are unaggregated).

molecule: total RNA

organism: Solanum lycopersicum

source_name: root

growth_protocol: Seeds were sterilized and sown in Profile calcined Clay media in 4-inch pots with a modified removable bottom. Plants were grown in Conviron  392 PGR15 growth chambers (Controlled Environments Ltd., Winnipeg, Manitoba, Canada).

extract_protocol:
For transcriptome profiling, root tissue from three individual plants was pooled together to yield one root sample per treatment-species combination per day on each of the three sampling days, and shoot tissue from the same three plants was pooled together to yield one shoot sample per treatment-species combination per day on each of the three sampling days.
RNAseq Library Preparation   RNAseq libraries were prepared using the method described by (Kumar et al., 2012). Briefly, for each library, the pooled root or shoot samples were homogenized in lysis and binding buffer containing beta-mercaptoethanol. Tissue was disrupted using a mortar and pestle and a Mini-beadbeater-96 high-throughput cell disruptor (BioSpec Products, Bartlesville, OK). Oligo (dT)25-coated Dynabeads (Ambion, Foster City, CA) were then added to the lysate, and mixed for 10 minutes to allow oligo (dT) beads to hybridize to poly-adenylated mRNA. cDNA was then synthesized and digested to ~300 bp fragments using NEBNext DNA fragmentase enzyme mix (NEB, Beverly, MA, USA). Library fragments greater than 300 bp were purified using Ampure XP solid phase reverse immobilization (SPRI) magnetic beads (Agencourt Bioscience, Beverly, MA, USA). For each library, one of the ninety-six unique barcoded adapters described in Kumar et al (2012) was ligated to each library, enabling multiplexing. cDNA was quantified using a SYBR-green based method on a plate reader, libraries were pooled, and fragment size and quality was checked using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).  Translating Ribosome Affinity Purification (TRAP)   To determine the effects of eCO2 on the translatome of shoot tissue, transgenic S. lycopersicum and S. pennellii expressing a FLAG-epitope on the ribosomal L18 (RPL18) under the 35S promoter (Ron et al., 2013) were grown in ambient and elevated [CO2] in the same conditions and chambers as described above. At 6 and 12 DAP, tissue was collected for the Translating Ribosome Affinity Purification (TRAP) protocol. Because the biomass of plant tissues in young seedlings was small, and because the TRAP populations were segregating, we pooled multiple plants (up to 15) together to ensure that adequate mRNA for library preparation could be collected via the ribosomal pulldown.   The TRAP procedure has been described by (Zanetti et al., 2005). Briefly, tissues from transgenic plants expressing the FLAG epitope was ground in liquid nitrogen using a mortar and pestle, and homogenized in polysome extraction buffer. Samples were clarified by centrifugation and filtration through Miracloth, and clarified extract was added to magnetic beads that were coated in anti-flag antibody. Beads and extract were incubated at 4˚C using a nutator for 2 hours, and washed 6-7 times with wash buffer. Polysomes bound to magnetic beads were then frozen at -80°C until RNAseq library preparation.   RNAseq libraries were prepared from TRAP polysomes using the method described by (Townsley et al., 2015). Lysis and binding buffer containing beta-mercaptoethanol was added to anti-flag magnetic beads and bound ribosomes, allowing elution of mRNA. mRNA was then hybridized to biotin-20nt-dT oligos, allowing pulldown of mRNA out of solution with the use of magnetic streptavidin beads. mRNA was then washed with three successive buffers, eluted off of beads at 80˚C, and a secondary wash was performed, by adding more biotin-20nt-dT oligos to the mRNA, repeating the bead pulldown, and the buffer washes. mRNA was then heat-fragmented, and first and second strand cDNA was synthesized. The optimal fragment size was selected using Ampure beads, and libraries were enriched using PCR.

treatment_protocol: Chambers were set at either ambient (400 ppm) or eCO2 (700 ppm), 325 μmol m-2 s-1 PPFD, 70% Relative humidity, 16:8 light: dark schedule, and 22° C at the Controlled Environment Facility at University of California, Davis. Plants were watered every 2-3 days with 40% Long-Ashton solution containing 6 mM NH4NO3. The location of flats within each chamber and the location of plants within each flat were rotated upon every watering, and CO2 treatment assignments were rotated between chambers at every experimental replication in order to avoid any experimental artifacts caused by differences between chambers.

tag: cultivar

value: ele

tag: day

tag: r

tag: pool

tag: lnrep

tag: tissue

value: root


title: R2_D09_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_shoot_Pool1_LnRep1.fq.gz

source_name: shoot

value: amb

value: shoot


title: R5_D12_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_root_Pool2_LnRep4.fq.gz

organism: Solanum pennellii


title: R2_D09_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_root_Pool2_LnRep4.fq.gz


title: R5_D12_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_root_Pool2_LnRep3.fq.gz


title: R5_D12_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_root_Pool2_LnRep2.fq.gz


title: R2_D09_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_root_Pool1_LnRep1.fq.gz


title: R2_D09_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_root_Pool2_LnRep3.fq.gz


title: R2_D09_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_root_Pool2_LnRep2.fq.gz


title: R5_D12_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_root_Pool2_LnRep1.fq.gz


title: R2_D06_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D09_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_shoot_Pool2_LnRep4.fq.gz


title: R2_D06_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R2_D06_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R2_D06_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_root_Pool2_LnRep4.fq.gz


title: R2_D06_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R2_D06_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_root_Pool2_LnRep3.fq.gz


title: R5_D09_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: R2_D09_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R2_D06_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D09_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: R2_D06_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_root_Pool1_LnRep1.fq.gz


title: R5_D09_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: R2_D06_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R2_D06_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R2_D09_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_root_Pool2_LnRep1.fq.gz


title: R5_D09_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_shoot_Pool1_LnRep1.fq.gz


title: R2_D06_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D09_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_root_Pool2_LnRep4.fq.gz


title: R2_D06_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_root_Pool1_LnRep1.fq.gz


title: R5_D09_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_root_Pool2_LnRep3.fq.gz


title: R2_D06_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D09_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_root_Pool2_LnRep2.fq.gz


title: R2_D06_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_root_Pool2_LnRep2.fq.gz


title: R2_D06_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_root_Pool2_LnRep4.fq.gz


title: R5_D09_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_root_Pool2_LnRep1.fq.gz


title: 3_Untreated

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Basecalls performed using bcl2FastQ v1.8.4.
Reads were aligned to the hg19 genome assembly using HISAT2.
Gene counts were quantified using htseq-count.
Genome_build: GRCh37/hg19 and respective gene annotation.
Supplementary_files_format_and_content: The Excel file includes raw counts of all genes for each sample.

organism: Homo sapiens

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in humidified incubator at 37°C and 5% CO2 in RPMI 1640 (supplemented: 1 mM sodium pyruvate, 10% FCS).

extract_protocol:
Total RNA was isolated and purified using Direct-zol™ RNA Kit (Zymo Research)
Library preparation was done using Illumina's TruSeq Stranded mRNA Library Preparation Kit following the manufacturer's instruction.

treatment_protocol: 1.5 x 10^6 cells were treated with respective compounds for 3 hours.

tag: cell type

tag: perturbation


title: R2_D06_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_root_Pool2_LnRep3.fq.gz


title: R5_D09_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_penn_root_Pool1_LnRep1.fq.gz


title: 3_MB3

value: ATRA (100 nM) and GSK-LSD1 (1 nM)


title: R5_D09_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_shoot_Pool2_LnRep4.fq.gz


title: R2_D06_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_root_Pool2_LnRep1.fq.gz


title: R2_D06_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_root_Pool2_LnRep2.fq.gz


title: 3_ATRA+GSK-LSD1

value: ATRA (100 nM)


title: R5_D09_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: LTF_33_HFD

city: Lyngby

first: Pankaj

last: Arora

email: sbrix@dtu.dk, sbp@bio.dtu.dk, panar@dtu.dk, panar.arora@sund.ku.dk

address: Søltofts Plads - blg. 224 room 218, DK-2800 Kgs. Lyngby

department: Department of Biotechnology and Biomedicine

country: Denmark

institute: Technical University of Denmark

description:
ReadCount.gene.matrix_LTF
FPKM.gene.matrix_LTF
TPM.gene.matrix_LTF

data_processing:
De-multiplexed raw data was provided by Novogene Corporation, China.
Cutadapt (v1.15) was used to remove sequencing adapters and low quality reads from the de-multiplexed raw data (cutadapt -j 1 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --mask-adapter --quality-base=33 --max-n=0.2 -o ....) . STAR (v2.6.0) and RSEM (Li nd Dewey BMC Bioinformatics 2011) were used to map and align the clean reads and perform transcript quantification, respectively.
After mapping transcripts to gene symbols, we obtained a gene count matrix with 47,729 genes of which 11,557 genes were not expressed in any samples and removed. Of the remaining 36,172 genes, 79 genes had duplicate gene symbols, and only the gene with the highest total read count was retained. To filter out lowly expressed genes, we filtered out genes that did not have more than five reads in at least six samples, leaving 14,015 genes for further analysis. Cell type deconvolution was made using BSEQ-sc v1.0 (Baron et al., Cell Systems 2016) and CIBERSORT (Newman et al., Nature Methods 2015). To remove gene count contributions from contaminating cell types, we weighed the read counts of all genes that were expressed by multiple cell types in Haber et al. by the cell type proportion estimated by BSEQ-sc. Furthermore, using the log10 read count distribution of Haber et al. we estimated the mode and the lower and upper read count cutoff that would contain 95% of the reads below and above the mode, respectively. Using the lower cutoff to exclude genes whose read counts were too low to confidently estimate tuft cell read proportions, we estimated the proportion of reads that originated from tuft cells and used this factor as an additional weight parameter when removing contaminating reads. Finally, we used the read count distribution of non-tuft cell marker genes (as identified in Haber et al., Nature 2017) in the Haber tuft cells to estimate which genes that were not expressed in tuft cells and thus could be removed; there were 853 genes with at least three reads in at least 20% of any non-tuft cell types and with at least three reads in less than 20% of tuft cells, and together with the non-tuft marker genes, these were removed from the dataset.
Genes were annotated with pathway information using Reactome (Fabregat et al., Nucleic Acid Research 2018), and differentially expressed genes and pathways were identified using SAM-seq v.1.0 (Li and Tibshirani, Statistical Methods in Medical Research). Differentially expressed genes that were not part of any Reactome pathway (termed orphan genes) were designated immune/metabolism-associated if they were annotated with either the GO term “GO:0008152 metabolic process” or “GO:0002376 immune system process”.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read count matrix, RPKM and TPM values for each sample

organism: Mus musculus

source_name: Small intestinal epithelial cells

extract_protocol:
For analyses of gene expression, RNA was extracted from cell suspensions of small intestinal tuft cells (EpCAM+CD45+ Siglec-F+). Total RNA concentration was measured, checked for quality and used for cDNA preparation by reverse transcription of 5.6 μL of purified RNA. cDNA was amplified using Smart-seq2 protocol (Picelli et al., Natue protocols 2014), purified, quantified, and checked for quality and library size.
Nextera XT DNA library preparation kit  (Illumina, FC-131-1096) was used with 1 ng purified cDNA for the construction of sequencing libraries.
cDNA libraries having insert sizes of 500-800 bp were used for paired-end sequencing on the Illumina NovaSeq 6000 sequencing platform (Novogene Corporation, China).

treatment_protocol: Small intestinal and epididymal (eWAT) white adipose tissue were dissected and digested in order to obtain single cell suspensions which were labeled with antibodies for flow cytometric analysis.

value: small intestinal tuft cells

tag: isolation method

value: FACS-sorted

tag: surface markers

value: EpCAM+CD45+ Siglec-F+

tag: feed type and feeding duration

value: HFD (60% Fat) 9 weeks


title: LTF_34_HFD


title: 3_ATRA+GSK-LSD1+MB3


title: R5_D09_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: 3_ATRA+MB3

value: GSK-LSD1 (1 nM) and MB3 (50 uM)


title: 3_GSK-LSD1

value: ATRA (100 nM) and GSK-LSD1 (1 nM) and MB3 (50 uM)


title: 2_Untreated

value: GSK-LSD1 (1 nM)


title: R5_D09_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_root_Pool2_LnRep4.fq.gz


title: LTF_31_HFD


title: LTF_32_HFD


title: R5_D09_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_shoot_Pool1_LnRep1.fq.gz


title: 3_ATRA

value: ATRA (100 nM) and MB3 (50 uM)


title: R2_D06_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_amb_M82_root_Pool1_LnRep1.fq.gz


title: R5_D09_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_root_Pool2_LnRep3.fq.gz


title: 2_GSK-LSD1


title: LTF_80_HFD


title: LTF_70_HFD


title: R5_D09_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: Wild type cisplatin resistant without collagen, biological rep1

type: RNA

city: Poznań

first: Radosław

last: Januchowski

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: University of Medical Sciences

hyb_protocol: Following fragmentation, 9.4 ug of cRNA were hybridized for 16 hr at 45C on PrimeView™ Human Genome U219 Array Strip. GeneChips were washed and stained in the Affymetrix Gene Atlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Gene Atlas Scanner.

data_processing: The data were analyzed with RMA using Transcription Analysis Console (version 4.0.1.36) which has implemented module for *.CEL to *.CHP files convertion.

label: biotin

source_name: W1CR cell line cultivated plastic surface

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip™ 3' IVT PLUS Reagent Kit Assay Manual Workflow, 2018, ThermoFisher Scientific).

growth_protocol: 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by purification on columns.

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: treatment

value: ovary


title: R5_D09_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_root_Pool2_LnRep2.fq.gz


title: Wild type cisplatin resistant with collagen, biological rep1

source_name: W1CR cell line cultivated on collagen surface

value: collagen


title: Wild type without collagen, biological rep1

source_name: W1 cell line cultivated on plastic surface


title: Wild type cisplatin resistant with collagen and cisplatin, biological rep1

source_name: W1CR cell line cultivated on collagen surface with addition of cisplatin

value: collagen and cisplatin


title: Wild type without collagen with cisplatin, biological rep1

source_name: W1 cell line cultivated on plastic surface with addition of cisplatin


title: Wild type with collagen, biological rep1

source_name: W1 cell line cultivated on collagen surface


title: 2_MB3


title: R5_D09_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_root_Pool2_LnRep1.fq.gz


title: R5_D06_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele


title: 2_ATRA+GSK-LSD1+MB3


title: R5_D06_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: R5_D09_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_penn_root_Pool1_LnRep1.fq.gz

value: root


title: LTF_8_HFD


title: LTF_50_HFD


title: 2_ATRA


title: 2_ATRA+GSK-LSD1


title: Wild type with collagen and cisplatin, biological rep1

source_name: W1 cell line cultivated on collagen surface with addition of cisplatin


title: Liver-17-060 [CTL060]

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

description:
Liver-17-060
processed data file: counts_liver.csv

data_processing:
Alignment to the Oar4.0 done with Bowtie2
Read counts was done using FeatureCounts
Differential expression analysis was performed with EdgeR
Genome_build: OAR4.0
Supplementary_files_format_and_content: readcounts

organism: Ovis aries

source_name: Liver

extract_protocol:
total RNA was extracted with Trizol per manufacturer's guidelines.
Afer polyA selection, paired-end RNA-sequencing with 75bp was done with a depth of 30M reads.

tag: gestational age (days)

tag: mechanical ventilation

value: Unventilated

tag: treament 1

tag: dose surfactant

tag: treament 2

tag: dose budesonide


title: LTF_7_HFD


title: R5_D06_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_shoot_Pool2_LnRep2.fq.gz

tag: day

value: shoot


title: 1_Untreated


title: Liver-17-059 [CTL059]

description:
Liver-17-059
processed data file: counts_liver.csv

tag: Sex

value: F


title: 2_ATRA+MB3


title: LTF_65_HFD


title: R5_D06_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_shoot_Pool2_LnRep1.fq.gz

tag: r

tag: pool


title: Liver-17-057 [CTL057]

description:
Liver-17-057
processed data file: counts_liver.csv

value: M


title: 1_GSK-LSD1


title: 1_MB3


title: Liver-17-058 [CTL058]

description:
Liver-17-058
processed data file: counts_liver.csv


title: R5_D06_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_root_Pool2_LnRep4.fq.gz

tag: lnrep

tag: tissue


title: R5_D06_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_shoot_Pool1_LnRep1.fq.gz


title: LTF_23_RFD

description:
ReadCount.gene.matrix_LTF
FPKM.gene.matrix_LTF
TPM.gene.matrix_LTF

tag: cell type

value: small intestinal tuft cells

value: RFD (10% Fat) 9 weeks


title: Wild type cisplatin resistant without collagen with cisplatin, biological rep1

source_name: W1CR cell line cultivated plastic surface with addition of cisplatin


title: LTF_24_RFD

tag: isolation method

value: FACS-sorted

value: EpCAM+CD45+ Siglec-F+


title: MeCP2_WT_input_rep5

city: Boston

first: Lisa

middle: D.

last: Boxer

state: MA

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

institute: Harvard Medical School

description:
10WT_10MeCP2_KO_H3K36me3_ChIPseq_input_gene_body_counts.txt
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSS_counts.txt
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt

library_source: genomic

data_processing:
Sequencing reads were trimmed with Trimmomatic (v0.36) to remove adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 genome with Bowtie2 (v2.2.9) with default parameters.
PCR duplicate reads were removed with Samtools (v0.1.19) rmdup.
Reads were extended to 250 bp (to approximate fragment length) with UCSC tools bedextendranges.
For each ChIP antibody, reads for each sample were randomly down-sampled to equal numbers using the GNU shuf utility.
ChIP-seq reads were quantified in the genomic regions specified in figure legends using Bedtools map (v2.26).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw ChIP read counts in either full gene bodies (transcription start site (TSS) to transcription termination site (TTS) of longest isoform), gene bodies excluding the first 3kb (TSS +3kb to TTS), or TSS (TSS -1kb to +1kb). For YY1 ChIP, file contains position of YY1 motifs in YY1 peaks.

molecule: genomic DNA

source_name: Forebrain tissue

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 8-to-12-week-old male mice and flash frozen. Tissue was homogenized in 1% formaldehyde and cross-linked for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 5 minutes at room temperature. Tissue was pelleted by spinning at 500 g for 5 minutes at 4°C, washed once with PBS, then spun again at 500 g for 5 minutes at 4°C. Cells were lysed by resuspending in L1 buffer (50 mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA pH 8, 1 mM EGTA pH 8, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitors) and rotating at 4°C for 10 minutes, then spun at 500 g for 5 minutes at 4°C. Nuclei were washed for 10 minutes at 4°C in L2 buffer (10 mM Tris pH 8, 200 mM NaCl, protease inhibitors), then spun at 500 g for 5 minutes at 4°C. Nuclei were resuspended in LB3 buffer (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine, protease inhibitors), and sonicated in a Diagenode Bioruptor (High Power, 60 cycles, 30 seconds on/45 seconds off). Insoluble material was removed by spinning at 16,000 g for 10 minutes at 4°C, and Triton X-100 was added to soluble chromatin at a final concentration of 1%. Chromatin was pre-cleared for two hours with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) Dynabeads, then incubated with Protein A or Protein G Dynabeads conjugated to antibodies overnight at 4°C. Antibodies used were: H3K27ac (Abcam ab4729), H3K36me3 (Abcam ab9050), H4K12ac (Millipore 07-595), H3K9ac (Millipore 06-942), H3K79me2 (Abcam ab3594), Pol II (Abcam ab817), Pol II Ser5p (Millipore 04-1572), and MeCP2 (Chen et al., 2003). Beads were washed twice with Low Salt Buffer (20 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with LiCl Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 1% NP-40, 250 mM LiCl, 1% sodium deoxycholate) and once with TE Buffer (50 mM Tris pH 8, 10 mM EDTA) at 4°C. Chromatin was eluted off beads by incubating in TE Buffer with 1% SDS at 65°C for one hour, and crosslinks were reversed by incubating overnight at 65°C. Chromatin was treated with RNase A for 30 minutes at 37°C and Proteinase K for 2 hours at 55°C. DNA was phenol-chloroform extracted and purified with the Qiagen PCR purification kit.
Libraries were generated using the NuGEN Ovation Ultralow System V2 following manufacturer instructions.

tag: strain

tag: age

value: 8 weeks

tag: gender

value: Male

tag: genotype

value: WT

tag: chip antibody


title: LTF_5_HFD

tag: surface markers

tag: feed type and feeding duration

value: HFD (60% Fat) 9 weeks


title: Liver-17-054 [BUD054]

description:
Liver-17-054
processed data file: counts_liver.csv

tag: gestational age (days)

tag: mechanical ventilation

value: Ventilated

tag: treament 1

value: Intratracheal Poractant alpha

tag: dose surfactant

tag: treament 2

value: Budesonide


title: 1_ATRA

tag: perturbation

value: ATRA (100 nM) and GSK-LSD1 (1 nM) and MB3 (50 uM)


title: Liver-17-051 [SUR051]

description:
Liver-17-051
processed data file: counts_liver.csv

tag: Sex

tag: dose budesonide


title: R5_D06_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_root_Pool2_LnRep2.fq.gz

value: ele

tag: day

tag: r

tag: pool

tag: lnrep

tag: tissue

value: root


title: LTF_40_RFD

tag: cell type

tag: isolation method


title: 1_ATRA+GSK-LSD1+MB3

value: ATRA (100 nM) and MB3 (50 uM)


title: R5_D06_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_root_Pool2_LnRep3.fq.gz


title: Liver-17-049 [SUR049]

description:
Liver-17-049
processed data file: counts_liver.csv

value: F


title: Liver-17-050 [BUD050]

description:
Liver-17-050
processed data file: counts_liver.csv


title: 1_ATRA+GSK-LSD1

value: ATRA (100 nM) and GSK-LSD1 (1 nM)


title: 1_ATRA+MB3

value: ATRA (100 nM)


title: R2_D06_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D06_ele_M82_shoot_Pool2_LnRep3.fq.gz

tag: cultivar

value: shoot


title: R5_D06_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_root_Pool1_LnRep1.fq.gz


title: LTF_6_HFD

value: small intestinal tuft cells

value: FACS-sorted

tag: surface markers

tag: feed type and feeding duration


title: LTF_21_RFD

value: EpCAM+CD45+ Siglec-F+

value: RFD (10% Fat) 9 weeks


title: Input Untreated

data_processing:
Basecalls performed using bcl2FastQ v1.8.4.
Reads were aligned to the hg19 genome assembly using bwa (Version: 0.7.12-r1039, Parameter: aln -q 20).
Alignments were filtered for PCR duplicates using PICARD tools (Version: 1.119)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BigWig files were created using deeptools (bamCoverage) and scores represent RPKM values in 50bp bins.

extract_protocol:
Cells were washed in PBS and fixed for 10 min in 1% formaldehyde. Fixation was stopped by incubation with 140 mM glycine for 5 min and cells were washed in PBS. Cell pellet was resuspended in fivefold pellet volume of hypotonic buffer (20 mM HEPES pH 7,9, 10 mM KCl, 10% Glycerol, 1 mM EDTA, 0.2% NP-40) and after 4 min centrifuged. Nuclei pellet was lysed in 350 µl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8,1, protease inhibitor cocktail) for 25 min on ice and subsequently DNA was shared by sonification (6 pulses, 50% amplitude, 30 sec pause in between) using a Branson digital sonifier W-250. By 15 min centrifugation at 15 000 rpm and 4 °C cell debris were removed. 150 µl of the supernatant were diluted with 1350 µl ChIP dilution buffer (0.01% SDS, 1,1% TritonX-100, 1,2 mM EDTA, 16,7 mM Tris-HCL pH 8,1, 167 mM NaCl) and subjected to 2 µg antibody or IgG control at 4 °C overnight.
Libraries were prepared with TruSeq ChIP Library Preparation Kit. Bead-based size selection was performed after TrueSeq  to enrich for fragments of 550bp.

treatment_protocol: Cells were treated for 1 hour with respective compounds.

value: AML M2 cell line HL-60

tag: chip antibody


title: LTF_30_RFD


title: LTF_10_RFD


title: R5_D06_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_penn_root_Pool2_LnRep1.fq.gz


title: Liver-17-032 [SUR032]

description:
Liver-17-032
processed data file: counts_liver.csv

tag: gestational age (days)

tag: mechanical ventilation

tag: treament 1


title: R5_D06_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb


title: R5_D06_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: Liver-17-031 [BUD031]

description:
Liver-17-031
processed data file: counts_liver.csv

value: Ventilated

tag: dose surfactant

tag: treament 2


title: LTF_4_RFD


title: LTF_22_RFD


title: Input ATRA+GSK-LSD1+MB3

tag: perturbation


title: Input ATRA+GSK-LSD1


title: R5_D06_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_shoot_Pool2_LnRep2.fq.gz

tag: day


title: Liver-17-048 [BUD048]

description:
Liver-17-048
processed data file: counts_liver.csv

tag: Sex

value: Intratracheal Poractant alpha

tag: dose budesonide


title: LTF_3_RFD

description:
ReadCount.gene.matrix_LTF
FPKM.gene.matrix_LTF
TPM.gene.matrix_LTF


title: Input ATRA+MB3


title: LTF_2_RFD


title: R5_D06_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_shoot_Pool2_LnRep1.fq.gz

tag: r

tag: pool

tag: lnrep


title: Liver-17-007 [SUR007]

description:
Liver-17-007
processed data file: counts_liver.csv

value: M


title: PVWM-17-061

description:
PVWM-17-061
processed data file: counts_pvwm.csv

source_name: PVWM

value: Unventilated


title: STF_64_HFD

description:
ReadCount.gene.matrix_STF
FPKM.gene.matrix_STF
TPM.gene.matrix_STF

tag: cell type

tag: isolation method

value: HFD (60% Fat) 9 weeks


title: R5_D06_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_shoot_Pool1_LnRep1.fq.gz

tag: tissue


title: PVWM-17-060

description:
PVWM-17-060
processed data file: counts_pvwm.csv


title: R5_D06_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_root_Pool2_LnRep4.fq.gz

value: root


title: PVWM-17-058

description:
PVWM-17-058
processed data file: counts_pvwm.csv


title: H3K9me2 Untreated

value: Anti-Di-Methyl Histone H3 (Lys9) (Cell Signaling, #9753)


title: H3K9me2 ATRA+GSK-LSD1+MB3

value: ATRA (100 nM) and GSK-LSD1 (1 nM) and MB3 (50 uM)


title: R5_D06_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_root_Pool2_LnRep3.fq.gz


title: PVWM-17-057

description:
PVWM-17-057
processed data file: counts_pvwm.csv


title: PVWM-17-054

description:
PVWM-17-054
processed data file: counts_pvwm.csv

value: Budesonide


title: STF_63_HFD

tag: surface markers

tag: feed type and feeding duration


title: STF_62_HFD


title: R5_D06_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_root_Pool2_LnRep2.fq.gz


title: STF_80_HFD


title: PVWM-17-051

description:
PVWM-17-051
processed data file: counts_pvwm.csv

tag: gestational age (days)

value: F


title: R5_D06_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_root_Pool2_LnRep1.fq.gz


title: R5_D06_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_penn_root_Pool1_LnRep1.fq.gz


title: H3K9ac Untreated

tag: chip antibody

value: Anti-Acetyl Histone H3 (Lys9) (Merk, #ABE18)


title: H3K9me2 ATRA+MB3

value: ATRA (100 nM) and MB3 (50 uM)


title: STF_70_HFD

value: small intestinal tuft cells

value: FACS-sorted


title: H3K9me2 ATRA

value: ATRA (100 nM)


title: STF_60_HFD

value: EpCAM+CD45+ Siglec-F+


title: H3K9ac ATRA+GSK-LSD1+MB3

value: AML M2 cell line HL-60


title: STF_50_HFD


title: Input ATRA


title: LTF_1_RFD

value: RFD (10% Fat) 9 weeks


title: H3K9me2 ATRA+GSK-LSD1

value: ATRA (100 nM) and GSK-LSD1 (1 nM)


title: PVWM-17-048

description:
PVWM-17-048
processed data file: counts_pvwm.csv

tag: mechanical ventilation

value: Ventilated

tag: treament 1

value: Intratracheal Poractant alpha


title: STF_8_HFD

value: HFD (60% Fat) 9 weeks


title: PVWM-17-032

description:
PVWM-17-032
processed data file: counts_pvwm.csv

tag: dose surfactant

tag: treament 2


title: R4_D12_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_shoot_Pool2_LnRep2.fq.gz

value: ele

tag: day

value: shoot


title: PVWM-17-031

description:
PVWM-17-031
processed data file: counts_pvwm.csv

tag: Sex


title: H3K9ac ATRA+MB3

tag: perturbation


title: STF_7_HFD


title: H3K9ac ATRA


title: STF_6_HFD


title: R4_D12_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_shoot_Pool2_LnRep1.fq.gz

tag: r


title: R4_D12_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_shoot_Pool1_LnRep1.fq.gz

tag: pool


title: STF_5_HFD

description:
ReadCount.gene.matrix_STF
FPKM.gene.matrix_STF
TPM.gene.matrix_STF


title: SIN3_KD+SAM-S_KD_rep3

city: Detroit

first: Lori

middle: Ann

last: Pile

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

description:
test
replicates 1,2 and 3 combined

data_processing:
Illumina bcl2fastq converter was used to demultiplex samples.
Tuxedo pipeline was used to allign reads to dm3, estimation of  transcripts and analyze differential expression. All steps were performed using default settings.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and expression fold change as determined by Cuffdiff.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila Schneider cell line 2 (S2) cells were cultured at 270C in Schneider's Drosophila medium (1x) + L-glutamine (Life Technologies) with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 mg/ml gentamycin.

extract_protocol:
Total RNA was isolated from treated S2 cells using the EZ1 RNA Universal Kit (Quiagen). Cells were disrupted and homogenized in 750 μl  QIAzol lysis reagent via bead-milling on the TissueLyser II (Qiagen). RNA was collected from the homogenate by chloroform exraction and purified on the EZ1 Advanced (Qiagen) with additional step to remove any residual DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with dsRNA targeting Sin3A and Sam-S genes for 4 days prior to RNA extraction

value: S2 cells

tag: genotype

value: wild type


title: PVWM-17-050

description:
PVWM-17-050
processed data file: counts_pvwm.csv

value: F

value: Budesonide

tag: dose budesonide


title: R4_D12_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_root_Pool2_LnRep4.fq.gz

tag: lnrep

value: root


title: PVWM-17-007

description:
PVWM-17-007
processed data file: counts_pvwm.csv

value: M


title: STF_24_RFD

tag: cell type

value: small intestinal tuft cells

tag: isolation method

value: FACS-sorted


title: R4_D12_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_shoot_Pool2_LnRep4.fq.gz

tag: tissue


title: PVWM-17-049

description:
PVWM-17-049
processed data file: counts_pvwm.csv

tag: gestational age (days)


title: SIN3_KD+SAM-S_KD_rep2

description:
test
replicates 1,2 and 3 combined


title: Sample 182: I2_3_L4

city: Stanford

first: Erin

last: Mitsunaga

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
FASTQ files were submitted to iRepertoire for analysis using their iRmap program (Wang et al., 2010).
Briefly, sequence reads were de-multiplexed according to barcode sequences at the 5’ end of reads from the BCR heavy constant regions. Reads were then trimmed according to their base qualities with a 2-base sliding window.
Trimmed paired-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm.
The merged reads were mapped using a Smith-Waterman algorithm to germline V, D, J, and C reference sequences downloaded from the IMGT web site (Lefranc, 2003).
To define the CDR3 region, the position of CDR3 boundaries of reference sequences from the IMGT database were migrated onto reads through mapping results, and the resulting CDR3 regions were extracted and translated into amino acids.
Genome_build: IMGT human BCR
Supplementary_files_format_and_content: Comma-separated values files were generated by iRepertoire for each sample.  Each files contains the nucleic acid and predicted amino acid sequence of the CDR3 regions, isotypes, assigned V, D, and J genes, and read counts.

source_name: B cells

extract_protocol:
Total RNA was extracted from flow cytometry-sorted human peripheral blood B cells with the Qiagen AllPrep RNA/DNA Micro Kit (Cat. # 80284) per the manufacturer's instructions.
Targeted RNA sequencing libraries were made using human B cell-specific primers from iRepertoire (Huntsville, AL) according to the company's instructions.  Briefly, two rounds of RT-PCR were performed for each chain type (heavy or light chain) and the resulting B cell receptor amplicons were sequenced.

value: B cells

value: Peripheral blood

tag: subset

value: Plasmacyte

tag: chain type

value: Light - Kappa and Lambda

tag: irepertoire barcode

tag: health status

value: Second Infection

tag: time point


title: R4_D12_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_shoot_Pool2_LnRep3.fq.gz

tag: day


title: R4_D12_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_root_Pool2_LnRep2.fq.gz

source_name: root


title: STF_23_RFD

tag: surface markers

value: EpCAM+CD45+ Siglec-F+

tag: feed type and feeding duration

value: RFD (10% Fat) 9 weeks


title: H3K9ac ATRA+GSK-LSD1

value: AML M2 cell line HL-60

tag: chip antibody

value: Anti-Acetyl Histone H3 (Lys9) (Merk, #ABE18)

tag: perturbation

value: ATRA (100 nM) and GSK-LSD1 (1 nM)


title: SIN3_KD+SAM-S_KD_rep1

description:
test
replicates 1,2 and 3 combined

value: S2 cells

tag: genotype

value: wild type


title: Sample 179: I2_3_H3

value: Memory

value: Heavy


title: R4_D12_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_root_Pool2_LnRep1.fq.gz

value: ele

tag: r

tag: pool

value: root


title: Sample 180: I2_3_L3

tag: cell type


title: STF_22_RFD

value: small intestinal tuft cells

tag: isolation method

value: FACS-sorted


title: SAM-S_KD_rep3

description:
test
replicates 1,2 and 3 combined

treatment_protocol: Cells were treated with dsRNA targeting Sam-S gene for 4 days prior to RNA extraction

tag: tissue


title: SAM-S_KD_rep1

description:
test
replicates 1,2 and 3 combined


title: STF_21_RFD


title: SAM-S_KD_rep2

description:
test
replicates 1,2 and 3 combined


title: STF_40_RFD


title: R4_D12_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_shoot_Pool2_LnRep4.fq.gz

source_name: shoot

value: amb

tag: lnrep

value: shoot


title: Sample 178: I2_3_L2

value: B cells

value: Peripheral blood

tag: subset

value: Naïve

value: Light - Kappa and Lambda


title: R4_D12_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_root_Pool1_LnRep1.fq.gz


title: Sample 177R: I2_3_H2R

tag: chain type

value: Second Infection


title: STF_20_RFD

value: EpCAM+CD45+ Siglec-F+

value: RFD (10% Fat) 9 weeks


title: R4_D12_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: SIN3_KD_rep3

description:
test
replicates 1,2 and 3 combined

treatment_protocol: Cells were treated with dsRNA targeting Sin3A gene for 4 days prior to RNA extraction

value: S2 cells


title: STF_10_RFD


title: Sample 181: I2_3_H4

value: Plasmacyte

tag: irepertoire barcode


title: Sample 177: I2_3_H2

tag: health status


title: SIN3_KD_rep2

description:
test
replicates 1,2 and 3 combined

value: wild type


title: R4_D12_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_penn_root_Pool2_LnRep3.fq.gz


title: SIN3_KD_rep1

description:
test
replicates 1,2 and 3 combined


title: STF_84_RFD


title: R4_D12_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: Sample 176: I2_3_L1

value: Immature

tag: time point


title: GFP_RNAi_rep3

description:
control
replicates 1,2 and 3 combined

treatment_protocol: Cells were treated with dsRNA against the GFP gene as a control for 4 days prior to RNA extraction


title: R4_D12_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_shoot_Pool1_LnRep1.fq.gz

tag: day


title: R4_D12_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: STF_4_RFD

tag: surface markers


title: Sample 175R: I2_3_H1R

value: Heavy


title: STF_3_RFD

tag: feed type and feeding duration


title: R4_D12_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_root_Pool2_LnRep4.fq.gz

value: root


title: Sample 174: I2_2_L4


title: R4_D12_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_root_Pool2_LnRep3.fq.gz


title: GFP_RNAi_rep1

description:
control
replicates 1,2 and 3 combined


title: H2009-Chip

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: Parental cell

data_processing:
Basecalls performed using CASAVA
All reads were mapped to reference genome using bowtie2
Calculating insert size and standard deviation performed using Picard tools
ChIP-Seq and ATAC-Seq peak calling was performed using MACS
Normalization and deferential peak analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10, hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads)

source_name: H2009 cells

growth_protocol: KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 or ctrl-sgRNA-3 and then selected by using 5ug/ml Blasticidin, to get the 4 ctrl lines; KP-Cas9 single clone was transfected with Asf1a sgRNA-1, sgRNA-2 and then selected by using 5ug/ml Blasticidin, and then picked up single clones with Asf1a KO. For each Asf1a sgRNA, we selected 2 clones for ATAC seq, so totally we have 4 Asf1a KO clones for ATAC seq. For H2009, we just used the parental cell line for ChIP-seq.

extract_protocol:
Directly sent cells to core for ATAC seq; Performed ChIP by using commercial available ChIP kit and then sent the purified DNA sample to the core for ChIP-seq
The NYU Genome Technology Center constructed the libries followed their standard protocol

treatment_protocol: Control group (control1, control2, control3, control4) is Asf1a WT; KO group (KO1_1, KO1_3, KO2_1, KO2_3) is Asf1a KO; H2009-Input is control for ChIP seq, H2009-Chip is chip sample.

value: Human lung cancer cell line H2009

tag: strain

value: Human

value: In vitro cultured cell line


title: R4_D12_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_root_Pool2_LnRep2.fq.gz

value: amb


title: GFP_RNAi_rep2

description:
control
replicates 1,2 and 3 combined


title: STF_1_RFD

description:
ReadCount.gene.matrix_STF
FPKM.gene.matrix_STF
TPM.gene.matrix_STF

source_name: Small intestinal epithelial cells

value: small intestinal tuft cells

value: FACS-sorted


title: H2009-Input

description: Parental cell


title: Sample 172: I2_2_L3

value: B cells

value: Peripheral blood

value: Memory


title: Sample 173: I2_2_H4

value: Second Infection


title: Sample 171: I2_2_H3


title: R4_D12_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_root_Pool2_LnRep1.fq.gz


title: IP_CENPA_SW480_rep2

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
To identify putative centromeric transcripts from the RIP-seq results, we followed a computational pipeline as described in Quenet, et al., (2016) Methods Enzymol, 573, 445-466. Briefly, raw reads in fastq format were cropped to remove low quality base calls from read ends with Trimmomatic (Bolger et al., 2014). These pre-processed reads were then used in a first pass alignment to the repeating rDNA subunit (U13369.1, retrieved from GenBank) with Bowtie2 (Langmead et al., 2012) in sensitive mode, to deplete ribosomal transcripts in silico. The unaligned reads from this process were used for further analysis. These reads were mapped to the Build 38 reference genome (hg38) using Tophat (Trapnell et al., 2012). The centromeric sequence included in this version of the reference allowed us to map reads deriving from centromeric transcripts. Libraries for SW480 samples and replicates 3 and 4 of HeLa were trimmed using cutadapt 1.18 and aligned with STAR 2.6.1 (Dobin et al., 2013).
Putative reference cenRNA transcripts were defined from replicate 1 and 2 alignments by reference-guided transcript assembly using Cufflinks (Trapnell et al., 2012). Cufflinks was then used to estimate their abundances in units of FPKM across all samples.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file of centromeric transcript abundaces in each sample, in units of fragments per kilobase per million mapped reads (FPKM).

source_name: SW480 cells

growth_protocol: HeLa and SW480 cells were grown at 37°C, 5% CO2, in Dulbecco's modified Eagle's medium high in glucose and L-glutamine (#11965; Thermo Fisher Scientific/Gibco, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (#26140-079; Thermo Fisher Scientific/Gibco) and 1X Pen/Strep solution (#10378-016; Thermo Fisher Scientific/Gibco).

extract_protocol:
Illumina (RS-122-2203)
RNAs associated to CENP-A or agarose bead (mock-IP) were purified and identified following the protocol described in (Quenet, et al., (2016) Methods Enzymol, 573, 445-466). Briefly, for each condition, five F175 flasks of HeLa cells at a final confluency of 80% were used per RIP-seq. Trypsinized cells were washed two times with cold 1X PBS; 0.1% Tween 20 (#P2287, Sigma-Aldrich), before fixation with 0.1% formaldehyde (#15680, Electron Microscopy Sciences, Hatfield, PA) in 1X PBS. The reaction was stopped by addition of 125mM glycine (#50046, Sigma-Aldrich). Then, nuclei were isolated in TM2 buffer (20mM Tris–HCl, pH 8.0 (#15568-025, Thermo Fisher Scientific); 2mM MgCl2 (#AM9530G, Thermo Fisher Scientific); 0.5mM PMSF (#78830, Sigma-Aldrich); 1X complete protease inhibitor cocktail (#05892953001, Roche, Indianapolis, IN) complemented with 0.5% NonidetTM P40 Substitute (NP40, #74385, Sigma-Aldrich) and 10mM Ribonucleoside Vanadyl Complex (RVC, #1402, New England Biolabs—NEB, Ipswich, MA), and washed in TM2 buffer complemented with 10mM RVC. Chromatin was MNase-digested (MNase, #N3755, Sigma-Aldrich) in 0.1M TE buffer (0.1M NaCl (#24740-011, Thermo Fisher Scientific); 10mM Tris–HCl, pH 8.0; 0.2mM EGTA (#03777, Sigma-Aldrich) in presence of 2mM CaCl2 (#746495, Sigma-Aldrich). After addition of 10mM EGTA to stop the MNase action, nuclear pellet was resuspended in 1mL low-salt buffer (0.5X PBS, 5mM EGTA, 0.5mM PMSF, 1X complete protease inhibitor cocktail) complemented with 50 units of murine RNase inhibitor (#M0314S, NEB), and chromatin was extracted overnight at 4°C in an end-over-end rotator. After centrifugation, the supernatant was precleared with 30μL of protein A/G Plus agarose beads (#sc-2003,Santa Cruz Biotechnology, Dallas, TX) for 30 min at 4°C in an end-over-end rotator, and then, incubated with the anti-CENP-A primary antibody or no antibody for a minimum of 4 hours and a maximum of 12 hours at 4°C in an end-over-end rotator. CENP-A/primary antibody complex and mock-IP sample were immunoprecipitated with 50μL of protein A/G plus agarose beads for 2 hours at 4°C on the end-over-end rotator. Beads were washed three times with 1mL low-salt buffer containing murine RNase inhibitor and complete protease inhibitor cocktail. To isolate immuno-precipitated RNA, RNA–protein complex was eluted (elution buffer: 1% SDS; 0.1M sodium bicarbonate (#S6014, Sigma-Aldrich), denaturated, treated sequentially with proteinase K (#AM2548, Thermo Fisher Scientific/Ambion) and DNaseI (#AM2222, Thermo Fisher Scientific/Ambion), and purified by phenol:chloroform:isoamylalcohol method. RNA concentration was determined by measurement on a UV-spectrophotometer and the quality of RNA was verified using a Bioanalyzer (#5067-1511, Agilent Technologies, Santa Clara, CA).
To prepare RIP samples for sequencing, libraries were constructed using Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012 & IP-202-1024, Illumina, San Diego, CA). RIP libraries were barcoded and run in multiplex on a HiSeq 2500 instrument (Illumina) by the NCI-Sequencing Core Facility. Cluster generation was performed using an Illumina HiSeq PE Cluster Kit v4 cBot (#PE-401-4001, Illumina). The sequencer was run for 125 cycles in paired-end mode. Libraries for SW480 samples and replicates 3 and 4 of HeLa were constructed with the Illumina TruSeq Stranded Total RNA Library Prep protocol, including rRNA depletion. These libraries were sequenced on an Illumina HiSeq4000 instrument for 150 cycles in paired-end mode.

treatment_protocol: Cells were synchronized by double thymidine block (0.5mM, #T9250; Sigma-Aldrich, Saint Louis, MO). After a first block of 19 hours, cells were released for 9 hours, followed by a second thymidine block of 16 hours. Then, cells were released for the appropriate time (10 hours for mitosis and 11 hours for early G1, as described previously in Quenet and Dalal, 2014).

tag: differentiation stage

value: early G1

tag: antibody

value: anti-CENP-A “3-19” [ab13939] (Abcam)

tag: fraction

value: chromatin


title: XBP1 LKO CT46 RNA-Seq rep1

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using Cufflinks (Mortazavi et al. 2008), HTSEQ and Bedtools (Quinlan et al. 2010) by default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python

source_name: LIVER

extract_protocol:
Mouse liver tissues were collected from XBP1Flox (n=2) and XBP1LKO (n=2) mice at 2h interval for a total of 48 hours under constant darkness condition. Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.
Extracted RNA samples underwent quality control assessment using the RNA Pico 6000 chip on Bioanalyzer 2100 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher). Strand-specific total mRNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGen) per the manufacturer’s instructions using 200ng of RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent).
The prepared libraries were pooled and sequenced using NoveSeq 6000 (Illumina), generating ~40 million 2×100 bp paired-end reads per samples. RNA-Seq library preparation and sequencing were performed at Univesity of Pittsburgh Medical Center (UPMC) Genome Center.

tag: gender

value: Male

value: C57BJ/L6 background

tag: age

value: 8-12 weeks of age

tag: genotype/variation

value: XBP1 LKO


title: XBP1 LKO CT44 RNA-Seq rep2


title: R4_D12_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_penn_root_Pool1_LnRep1.fq.gz

tag: r

tag: pool

tag: tissue

value: root


title: XBP1 LKO CT46 RNA-Seq rep2


title: IP_CENPA_rep4

source_name: HeLa cells


title: Sample 170: I2_2_L2

tag: cell type

tag: subset

value: Naïve

tag: chain type

value: Light - Kappa and Lambda


title: Sample 175: I2_3_H1

value: Immature

value: Heavy

tag: irepertoire barcode

tag: health status

tag: time point


title: Input_SW480_rep2


title: Sample 169: I2_2_H2


title: Input_rep4


title: R4_D09_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele

tag: day

tag: lnrep

value: shoot


title: Sample 168: I2_2_L1

value: B cells

value: Peripheral blood


title: XBP1 LKO CT42 RNA-Seq rep1

tag: strain


title: XBP1 LKO CT44 RNA-Seq rep1


title: R4_D09_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: Sample 167: I2_2_H1

value: Second Infection


title: IP_CENPA_SW480_rep1

tag: differentiation stage

value: early G1

tag: antibody


title: R4_D09_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: IP_CENPA_rep3

value: anti-CENP-A “3-19” [ab13939] (Abcam)

tag: fraction


title: R4_D09_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample 166: I2_1_L4

value: Plasmacyte


title: XBP1 LKO CT40 RNA-Seq rep1

tag: gender

value: Male

tag: age


title: R4_D09_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_shoot_Pool1_LnRep1.fq.gz

tag: r


title: Sample 164: I2_1_L3

value: Memory


title: XBP1 LKO CT38 RNA-Seq rep2

value: C57BJ/L6 background

value: 8-12 weeks of age

tag: genotype/variation


title: Input_rep3

value: chromatin


title: XBP1 LKO CT38 RNA-Seq rep1

value: XBP1 LKO


title: R4_D09_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_root_Pool2_LnRep3.fq.gz

tag: pool

tag: tissue

value: root


title: XBP1 LKO CT36 RNA-Seq rep2


title: Sample_118564

city: Ann Arbor

first: Benjamin

middle: H.

last: Singer

state: Mi

address: 109 Zina Pitcher Place

department: Internal Medicine Division of Pulmonary and Critical Care Medicine

institute: University of Michigan

data_processing:
Raw count data were processed by the University of Michigan Bioinformatics Core.
Read files were concatenated into a single fastq file for each sample. Raw read quality was checked using the program FastQC version v0.11.3 to identify potential quality problems from features of the data (e.g. low quality score, over-expressed sequences, and inappropriate GC content).
Reads were aligned to the reference genome including mRNAs and lncRNAs (UCSC genome build hg19) using both TopHat version 2.0.13 and Bowtie2 version 2.2.1. Default settings were used for alignment, with the exception of “--b2-very-sensitive”.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be used for all analyses.
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation, normalization, and differential expression analysis, using UCSC hg19 as the reference genome sequence. Within Cufflinks/Cuffdiff the following parameter settings were used: “--multi-read-correct”, “--compatible-hits-norm”, and “--upper-quartile–norm”.
Diagnostic plots were generated using the CummeRbund R package.
The differential expression analysis was performed by the University of Michigan Bioinformatics Core facility using their own internally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, differentially expressed genes and transcripts were identified based on three criteria: test status = “OK”, FDR ≤ 0.05, and fold change ≥ ± 0.5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count data for each Sample and has been filtered and normalized VST using the R package deseq2

source_name: parietal cortex gray matter

extract_protocol:
RNA was extracted from frozen post-mortem tissue using a standard Phenol Chloroform protocol.
cDNA libraries were prepared using the pico-input rRNA depletion cDNA kit (Takara Bio, Mountain View, CA), RNA libraries were subsequently prepared for sequencing using standard Illumina protocols

value: Brain

tag: case/control

value: NonSepsis

tag: biologic sex

value: M


title: R4_D09_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_root_Pool2_LnRep2.fq.gz

value: ele


title: XBP1 LKO CT42 RNA-Seq rep2


title: Sample_118563


title: XBP1 LKO CT36 RNA-Seq rep1


title: XBP1 LKO CT34 RNA-Seq rep2


title: R4_D09_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_root_Pool1_LnRep1.fq.gz


title: Sample 162: I2_1_L2

tag: cell type

value: B cells

tag: subset

value: Naïve

tag: chain type

value: Light - Kappa and Lambda

tag: irepertoire barcode


title: Sample 161R: I2_1_H2R

value: Peripheral blood

value: Heavy

tag: health status

value: Second Infection

tag: time point


title: R4_D09_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_root_Pool2_LnRep1.fq.gz

tag: day

tag: lnrep


title: Sample 161: I2_1_H2


title: Sample_118561


title: XBP1 LKO CT34 RNA-Seq rep1

value: Male

tag: strain


title: Sample_118560

value: Sepsis


title: XBP1 LKO CT40 RNA-Seq rep2

tag: gender

value: C57BJ/L6 background


title: Input_SW480_rep1

tag: differentiation stage

value: early G1

tag: antibody

tag: fraction


title: R4_D09_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_penn_root_Pool2_LnRep4.fq.gz

tag: r

tag: pool


title: Sample 160: I2_1_L1

tag: tissue

value: Immature


title: Sample_118557

tag: case/control

tag: biologic sex

value: F

tag: age


title: R4_D09_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb

value: shoot


title: Sample 163: I2_1_H3

tag: cell type

tag: subset

value: Memory

tag: chain type


title: Sample_118556

value: Brain


title: R4_D09_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: Sample 158: H17_L4

value: Plasmacyte

tag: irepertoire barcode

tag: health status

value: Healthy

tag: time point


title: Sample 159: I2_1_H1

value: B cells


title: Sample 165: I2_1_H4


title: R4_D09_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_shoot_Pool2_LnRep3.fq.gz

tag: day

tag: lnrep


title: XBP1 LKO CT30 RNA-Seq rep2

tag: gender

tag: strain

value: 8-12 weeks of age

tag: genotype/variation

value: XBP1 LKO


title: R4_D09_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_shoot_Pool2_LnRep1.fq.gz

tag: r


title: XBP1 LKO CT32 RNA-Seq rep1


title: Sample_118553

value: NonSepsis

value: M


title: XBP1 LKO CT30 RNA-Seq rep1

value: Male


title: Sample_118552

value: Sepsis


title: Sample 157: H17_H4

value: Peripheral blood

value: Heavy


title: Sample_118551


title: R4_D09_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_shoot_Pool1_LnRep1.fq.gz

tag: pool


title: XBP1 LKO CT28 RNA-Seq rep2

value: C57BJ/L6 background


title: R4_D09_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_root_Pool2_LnRep4.fq.gz

tag: tissue

value: root


title: Sample 156: H17_L3

value: Light - Kappa and Lambda


title: Sample 155: H17_H3


title: R4_D09_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_root_Pool2_LnRep3.fq.gz

value: amb


title: Sample 153R: H17_H2R

value: Naïve


title: Sample_118550

value: Brain

tag: case/control

value: F


title: XBP1 LKO CT26 RNA-Seq rep2


title: Sample 154: H17_L2

value: Healthy


title: XBP1 LKO CT32 RNA-Seq rep2


title: R4_D09_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_root_Pool2_LnRep2.fq.gz


title: Sample_118549

tag: biologic sex


title: Sample_118547

tag: age


title: R4_D09_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_root_Pool1_LnRep1.fq.gz


title: XBP1 LKO CT26 RNA-Seq rep1


title: XBP1 LKO CT24 RNA-Seq rep1


title: XBP1 LKO CT22 RNA-Seq rep2


title: R4_D06_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_shoot_Pool2_LnRep2.fq.gz

value: ele

value: shoot


title: Sample 153: H17_H2

tag: cell type

value: B cells


title: XBP1 LKO CT28 RNA-Seq rep1

value: 8-12 weeks of age

value: XBP1 LKO


title: Sample_117933

value: NonSepsis

value: M


title: Sample_117934


title: XBP1 LKO CT20 RNA-Seq rep2

value: Male


title: XBP1 LKO CT24 RNA-Seq rep2


title: Sample 152: H17_L1

value: Peripheral blood

tag: subset

value: Immature


title: R4_D06_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_shoot_Pool2_LnRep4.fq.gz


title: Sample_117937

value: Sepsis


title: Sample 151: H17_H1

tag: chain type

value: Heavy


title: R4_D06_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: Sample 149: H16_H4

value: Plasmacyte

tag: irepertoire barcode


title: XBP1 LKO CT22 RNA-Seq rep1

value: C57BJ/L6 background


title: Sample 148: H16_L3

value: Memory

value: Light - Kappa and Lambda

tag: health status


title: Sample_117928

value: Brain

value: F


title: R4_D06_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_shoot_Pool1_LnRep1.fq.gz

value: ele

value: shoot


title: XBP1 LKO CT20 RNA-Seq rep1

value: 8-12 weeks of age


title: Sample_117925


title: Sample_117924


title: R4_D06_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample_117938


title: Sample 146: H16_L2

value: B cells

value: Naïve

value: Healthy

tag: time point


title: XBP1 LKO CT18 RNA-Seq rep1

value: Male

value: XBP1 LKO


title: R4_D09_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_penn_root_Pool2_LnRep1.fq.gz

value: amb

tag: day

value: root


title: Sample_118546

value: Sepsis


title: Sample_117922

value: M


title: XBP1 LKO CT18 RNA-Seq rep2

value: C57BJ/L6 background


title: R4_D06_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_root_Pool2_LnRep3.fq.gz

tag: lnrep


title: R4_D06_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_root_Pool2_LnRep2.fq.gz


title: R4_D06_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_root_Pool2_LnRep1.fq.gz


title: Sample 150: H16_L4

value: Peripheral blood

value: Plasmacyte


title: Sample 147: H16_H3

value: Memory

value: Heavy


title: Sample 145: H16_H2


title: XBP1 LKO CT16 RNA-Seq rep2

tag: gender


title: Sample 144: H16_L1

value: Immature

value: Light - Kappa and Lambda


title: Sample_117920

value: Brain

value: F


title: Sample 145R: H16_H2R

value: B cells

value: Naïve


title: XBP1 LKO CT14 RNA-Seq rep1

value: Male

tag: strain

value: 8-12 weeks of age


title: XBP1 LKO CT14 RNA-Seq rep2

tag: genotype/variation

value: XBP1 LKO


title: Sample_117921

value: NonSepsis


title: Sample 143: H16_H1

value: Healthy


title: R4_D06_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb

tag: r

value: shoot


title: XBP1 LKO CT16 RNA-Seq rep1

value: C57BJ/L6 background


title: R4_D06_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_root_Pool1_LnRep1.fq.gz

value: ele

tag: pool

value: root


title: R4_D06_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_shoot_Pool2_LnRep3.fq.gz

tag: tissue


title: XBP1 LKO CT12 RNA-Seq rep2


title: Sample_117923

tag: case/control

value: Sepsis


title: Sample 142: H15_L4

value: Peripheral blood

value: Plasmacyte


title: Sample 141R: H15_H4R

value: Heavy


title: Total CD45+ cells from obese group

city: New York

first: Emily

last: Brown

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
single cell 3' gene counting, Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene expression by cell, file with barcodes and file with expressed genes.  Files are ready to be imported into Seurat package or similar.

molecule: polyA RNA

source_name: visceral adipose tissue

extract_protocol: Perigonadal adipose was isolated and washed with ice-cold PBS. Adipose was then minced to 2–3 mm pieces, added 4 mL of enzymatic digestion mix (1 mg/mL bovine-serum albumin, 0.77 mg/mL Liberase, 15.8 mU Hyaluronidase, 25 mU DNAse1 in Hanks’ Balanced Salt solution) and transferred to gentleMACS C-tubes. Tissue was then dissociated using the gentleMACS Octo Dissociator, program name: mr_adipose_01 , ran 3 times. Suspensions were subsequently filtered with a 100 µm cell strainer, washed with ice-cold PBS and stained for cell-sorting. Live CD45+ cells were sorted out using BD FACSAriaIII into DMEM containing 10% FBS. After centrifugation, cells were resuspended in final concentration of ~500 cells/µL in 1X HBSS containing 0.04% BSA to minimize cell loss and aggregation. ~12,000 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3' Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

value: visceral adipose tissue

value: CD45+ cells

tag: diet

value: obese


title: Sample 142R: H15_L4R

value: B cells

value: Light - Kappa and Lambda


title: XBP1 LKO CT10 RNA-Seq rep1

value: Male

tag: age

value: 8-12 weeks of age

value: XBP1 LKO


title: Total CD45+ cells from CR group

tag: cell type

value: Life-long caloric restriction


title: Handpad, KO_3

city: Irvine

first: Ghaidaa

last: Kashgari

address: 250 sprague Hall

institute: University of California Irvine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Kallisto
FastqC for sequencing quality
Kallisto for alignemnt and mapping
Edgar for differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Embryonic handpad tissue at E14.5

extract_protocol:
RNeasy Micro Kit-QIAGEN
Libraries were prepared according to Illumina's instructions
Illumina TruSeq® Stranded mRNA

tag: developmental stage

value: handpad

tag: genotype


title: R4_D06_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_shoot_Pool2_LnRep2.fq.gz

value: amb

value: shoot


title: XBP1 LKO CT12 RNA-Seq rep1

value: C57BJ/L6 background


title: XBP1 LKO CT8 RNA-Seq rep2


title: XBP1 LKO CT10 RNA-Seq rep2


title: R4_D06_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample 140: H15_L3

tag: subset

value: Memory

tag: chain type

tag: irepertoire barcode

value: Healthy


title: Sample 141: H15_H4

value: Peripheral blood

value: Plasmacyte

tag: health status

tag: time point


title: R4_D06_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_shoot_Pool1_LnRep1.fq.gz

tag: day

tag: lnrep


title: Handpad, WT_3

tag: strain

value: WT


title: Sample 139R: H15_H3R

value: Heavy


title: R4_D06_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_penn_root_Pool2_LnRep4.fq.gz

value: ele

tag: r

value: root


title: Sample 139: H15_H3

value: B cells


title: R4_D06_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_root_Pool2_LnRep2.fq.gz

tag: pool


title: XBP1 LKO CT8 RNA-Seq rep1

tag: gender

value: Male

tag: genotype/variation


title: Sample 140R: H15_L3R

tag: tissue

value: Light - Kappa and Lambda


title: Handpad, KO_2


title: R4_D06_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_root_Pool2_LnRep1.fq.gz


title: R4_D06_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_root_Pool1_LnRep1.fq.gz


title: R4_D06_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_root_Pool2_LnRep3.fq.gz


title: Sample 138: H15_L2

value: Naïve


title: KO2_3

description: Asf1a KO

source_name: KP cells with Asf1a KO

value: KP tumor cells

value: In vitro cultured cell line


title: Handpad, WT_1

value: handpad


title: XBP1 LKO CT6 RNA-Seq rep2

tag: age

value: 8-12 weeks of age

value: XBP1 LKO


title: Sample 137R: H15_H2R

tag: cell type


title: R4_D06_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_penn_root_Pool2_LnRep4.fq.gz

value: amb


title: Handpad, WT_2

tag: developmental stage


title: XBP1 LKO CT6 RNA-Seq rep1

value: C57BJ/L6 background


title: XBP1 LKO CT2 RNA-Seq rep2


title: Sample 138R: H15_L2R

value: Peripheral blood

value: Healthy


title: R3_D12_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_shoot_Pool2_LnRep3.fq.gz

value: shoot


title: Sample 137: H15_H2

value: Heavy


title: XBP1 LKO CT4 RNA-Seq rep2


title: Sample 136R: H15_L1R

value: Immature


title: XBP1 LKO CT4 RNA-Seq rep1


title: KO1_1

description: Asf1a KO


title: control4

description: Asf1a WT

source_name: KP cells with Asf1a WT


title: KO2_1

description: Asf1a KO


title: R3_D12_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: ele


title: WT CT46 RNA-Seq rep2

value: WT


title: KO1_3

description: Asf1a KO


title: Sample 134: H14_L4

value: B cells

value: Plasmacyte


title: R3_D12_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: R3_D12_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_root_Pool2_LnRep3.fq.gz

value: root


title: control2

description: Asf1a WT

value: KP tumor cells


title: XBP1 LKO CT2 RNA-Seq rep1

value: Male


title: WT CT44 RNA-Seq rep2


title: XBP1 LKO CT0 RNA-Seq rep2


title: R3_D12_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample 133: H14_H4


title: KO_plusPD1

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: KP lung tumors

growth_protocol: KP-WT or KP-Asf1a KO tumor cells were intravenously injected into B6 mice and lung tumor formation was monitored by MRI scan.

extract_protocol:
Mice were humanely euthanized, and mouse lungs were perfused using sterile PBS through heart perfusion from the left ventricle. The whole lung was cut and minced into small pieces followed by digestion in collagenase D (Sigma) and DNase I (Sigma) in Hank’s Balanced Salt Solution (HBSS) at 37°C for 30 minutes. After incubation, the digested tissue was subjected to a 70-μm cell strainer (ThermoFisher Scientific) to obtain single-cell suspensions. Live cell swere then sorted using DAPI  staining. Cells were then resuspended into single cells at a concentration of 1 x 106 per ml in 1X PBS with 0.4% BSA for 10x genomics processing.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: KP-WT or KP-Asf1a KO tumors were treated with isotype IgG (control) or anti-PD-1 (clone 29F.1A12, 200 ug/mouse, three times a week) for one week.

tag: genotye/variation

value: mouse NSCLC

tag: treatment

value: KP-Asf1a KO

tag: tag


title: R3_D12_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_root_Pool2_LnRep1.fq.gz


title: WT CT44 RNA-Seq rep1

value: 8-12 weeks of age


title: Handpad, KO_1

value: handpad

tag: genotype


title: Sample 136: H15_L1

tag: subset

tag: chain type

value: Light - Kappa and Lambda

tag: irepertoire barcode

tag: health status


title: XBP1 LKO CT0 RNA-Seq rep1

tag: strain

value: C57BJ/L6 background

value: XBP1 LKO


title: R3_D12_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_shoot_Pool1_LnRep1.fq.gz

tag: day

tag: r

tag: lnrep

value: shoot


title: Sample 135R: H15_H1R

value: Peripheral blood

value: Heavy

value: Healthy

tag: time point


title: control3

description: Asf1a WT

tag: tissue

value: In vitro cultured cell line


title: R3_D12_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb

tag: pool


title: Sample 130: H14_L2

tag: cell type

value: B cells

value: Naïve


title: Sample 135: H15_H1

value: Immature


title: R3_D12_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_root_Pool2_LnRep4.fq.gz

value: ele

value: root


title: control1

description: Asf1a WT

value: KP tumor cells


title: WT CT46 RNA-Seq rep1

tag: gender

value: Male

tag: age

value: 8-12 weeks of age

tag: genotype/variation

value: WT


title: Sample 129R: H14_H2R


title: Sample 132: H14_L3

value: Memory

value: Light - Kappa and Lambda


title: KO

tag: genotye/variation

value: mouse NSCLC

tag: treatment

value: KP-Asf1a KO

tag: tag

value: IgG (control)


title: WT CT42 RNA-Seq rep2

value: C57BJ/L6 background


title: R3_D12_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_root_Pool1_LnRep1.fq.gz


title: R3_D12_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_shoot_Pool2_LnRep1.fq.gz

value: shoot


title: Sample 128: H14_L1

value: Peripheral blood

tag: subset

tag: chain type

value: Healthy


title: R3_D12_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_shoot_Pool1_LnRep1.fq.gz

value: amb


title: Sample 131: H14_H3

value: B cells

value: Heavy

tag: irepertoire barcode

tag: health status


title: Ctrl_plusPD1

value: KP-WT


title: Ctrl


title: Sample 127: H14_H1

value: Immature


title: WT CT42 RNA-Seq rep1

value: Male

tag: strain


title: R3_D12_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_shoot_Pool2_LnRep3.fq.gz

tag: day

tag: r


title: WT CT40 RNA-Seq rep2

value: 8-12 weeks of age


title: WT CT40 RNA-Seq rep1

value: WT


title: R3_D12_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_penn_root_Pool2_LnRep2.fq.gz

value: ele

tag: lnrep

value: root


title: R3_D12_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_root_Pool2_LnRep4.fq.gz

tag: tissue


title: R3_D12_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_shoot_Pool2_LnRep2.fq.gz

tag: pool


title: WT CT38 RNA-Seq rep2


title: WT CT38 RNA-Seq rep1


title: Rectal biopsy 268

city: CLEVELAND

first: Matthew

last: Kalady

state: OHIO

address: 9500 EUCLID AVE

department: Cancer Biology Department

institute: CLEVELAND CLINIC

description: Gene expression in pretreated rectal cancer biopsy measured in frozen tissue

hyb_protocol: 1.5µg of biotinylated cRNA were incubated 5 minutes at 65°C before being mixed with 20µL hybridation mix provided by the kit (Illumina, San Diego, California, USA). After being placed into the chamber, the beadchip were loaded with 30uL of cRNA per sample.  The chamber is placed 17hrs at 58°C.  Beadchips are then washed with 250mL of the E1BC solution (Illumina) before a second wash at high temperature (55°C). The beadchips are rinced with fresh E1BC buffer then submerged for 10min with 100% ethanol. The beadcips are washed for a second time at room temperature and blocked with buffer provided by the kit.

scan_protocol: Slides were scanned immediately after washing on the Beadarray Reader (illumina) with Sentrix type 6x2and Direct hyb settings. Dye chennal is set to green with green PMT sets to 100% and gain to 0.5. After measurment of the tilt and alignment of the beadchips, scann is completed and .Tiff uncompressed images are then generated

data_processing: The scanned images with .tiff format were analyzed with Beadstudio Gene expression module v3.4 using default parameters tu quantify floresence intensity and substract the background for each beadchips analyzed.

source_name: Frozen rectal cancer biopsy

label_protocol: The Biotin-labeling was done during cRNA convertion using the  TotalPrepTM RNA amplification kit (Illumina, San Diego, California, USA) . Briefly, 100ng of mRNAs were used for a two-steps reverse transcription reaction and being converted into cDNA. After elution, the cDNA are converted into cRNA using biotin-NTP mix and then purified with a filter cartbridge. After hybridization and blockage, Biotin-labeled cRNA are incubated in streptavidin-Cy3 buffer provided in the kit at room temperature for 10 min and then washed with E1BC buffer provided in the kit and dried.

extract_protocol: The mRNA were extracted from the 12 slices/biopsy using the RNAqueous Kit (Ambion, Austin, Texas, USA) according the manufacturer's protocol. Then samples were treated with  TURBO DNA‐free  (Ambion, Austin, Texas, USA) to ensure a complete degradation of genomic DNA. Concentrations of mRNAs were determined with Nanodrop (ThermoFisher, Waltham, Massachusetts, USA) and quality of the extractions was assessed by 260/280nm readings. Integrity of mRNAs was verified by migration on agarose gel 1%.

treatment_protocol: Freshly harvested, the biopsies were snap frozen at -80°C. The frozen biopsies were then embadded in medium for frozen specimen to ensure optimal cutting temperature (O.C.T). Per biopsy, 12 slices of 10µm each were cut and used for mRNA extraction.

tag: subject status

value: patient with rectal adenocarcinoma

tag: ajcc score

tag: overall survival (in days)

tag: dead (1)/alive(0)


title: Sample 126: H13_L4

tag: cell type

value: Plasmacyte

value: Light - Kappa and Lambda

tag: time point


title: Rectal biopsy 277

tag: gender

value: Female

tag: age


title: WT CT36 RNA-Seq rep1

value: C57BJ/L6 background

tag: genotype/variation


title: R3_D12_amb_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_root_Pool2_LnRep3.fq.gz

data_processing:
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference transcriptome of S. lycopersicum (v3.2) using bowtie with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: ITAG3.2 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: comma separated files (one for RNA-Seq another for TRAP-Seq data) with raw counts for each sample (RNASeq tech reps are unaggregated).

extract_protocol:
For transcriptome profiling, root tissue from three individual plants was pooled together to yield one root sample per treatment-species combination per day on each of the three sampling days, and shoot tissue from the same three plants was pooled together to yield one shoot sample per treatment-species combination per day on each of the three sampling days.
RNAseq Library Preparation   RNAseq libraries were prepared using the method described by (Kumar et al., 2012). Briefly, for each library, the pooled root or shoot samples were homogenized in lysis and binding buffer containing beta-mercaptoethanol. Tissue was disrupted using a mortar and pestle and a Mini-beadbeater-96 high-throughput cell disruptor (BioSpec Products, Bartlesville, OK). Oligo (dT)25-coated Dynabeads (Ambion, Foster City, CA) were then added to the lysate, and mixed for 10 minutes to allow oligo (dT) beads to hybridize to poly-adenylated mRNA. cDNA was then synthesized and digested to ~300 bp fragments using NEBNext DNA fragmentase enzyme mix (NEB, Beverly, MA, USA). Library fragments greater than 300 bp were purified using Ampure XP solid phase reverse immobilization (SPRI) magnetic beads (Agencourt Bioscience, Beverly, MA, USA). For each library, one of the ninety-six unique barcoded adapters described in Kumar et al (2012) was ligated to each library, enabling multiplexing. cDNA was quantified using a SYBR-green based method on a plate reader, libraries were pooled, and fragment size and quality was checked using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).  Translating Ribosome Affinity Purification (TRAP)   To determine the effects of eCO2 on the translatome of shoot tissue, transgenic S. lycopersicum and S. pennellii expressing a FLAG-epitope on the ribosomal L18 (RPL18) under the 35S promoter (Ron et al., 2013) were grown in ambient and elevated [CO2] in the same conditions and chambers as described above. At 6 and 12 DAP, tissue was collected for the Translating Ribosome Affinity Purification (TRAP) protocol. Because the biomass of plant tissues in young seedlings was small, and because the TRAP populations were segregating, we pooled multiple plants (up to 15) together to ensure that adequate mRNA for library preparation could be collected via the ribosomal pulldown.   The TRAP procedure has been described by (Zanetti et al., 2005). Briefly, tissues from transgenic plants expressing the FLAG epitope was ground in liquid nitrogen using a mortar and pestle, and homogenized in polysome extraction buffer. Samples were clarified by centrifugation and filtration through Miracloth, and clarified extract was added to magnetic beads that were coated in anti-flag antibody. Beads and extract were incubated at 4˚C using a nutator for 2 hours, and washed 6-7 times with wash buffer. Polysomes bound to magnetic beads were then frozen at -80°C until RNAseq library preparation.   RNAseq libraries were prepared from TRAP polysomes using the method described by (Townsley et al., 2015). Lysis and binding buffer containing beta-mercaptoethanol was added to anti-flag magnetic beads and bound ribosomes, allowing elution of mRNA. mRNA was then hybridized to biotin-20nt-dT oligos, allowing pulldown of mRNA out of solution with the use of magnetic streptavidin beads. mRNA was then washed with three successive buffers, eluted off of beads at 80˚C, and a secondary wash was performed, by adding more biotin-20nt-dT oligos to the mRNA, repeating the bead pulldown, and the buffer washes. mRNA was then heat-fragmented, and first and second strand cDNA was synthesized. The optimal fragment size was selected using Ampure beads, and libraries were enriched using PCR.


title: Sample 129: H14_H2

value: Peripheral blood

tag: subset

value: Naïve

tag: chain type

tag: irepertoire barcode


title: WT CT36 RNA-Seq rep2

tag: strain


title: Sample 125: H13_H4

tag: health status

value: Healthy


title: Sample 124: H13_L3

value: B cells

value: Memory


title: WT CT34 RNA-Seq rep1


title: WT CT34 RNA-Seq rep2


title: R3_D12_amb_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_root_Pool2_LnRep1.fq.gz

value: amb

tag: day

tag: r

tag: lnrep


title: WT CT32 RNA-Seq rep2


title: R3_D12_amb_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_root_Pool1_LnRep1.fq.gz

tag: pool

tag: tissue


title: Sample 122: H13_L2


title: R3_D09_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_shoot_Pool2_LnRep4.fq.gz

value: shoot


title: Sample 121R: H13_H2R

value: Heavy


title: WT CT30 RNA-Seq rep2

value: Male

value: 8-12 weeks of age


title: R3_D09_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_shoot_Pool2_LnRep3.fq.gz

value: ele


title: Rectal biopsy 252

tag: subject status

tag: ajcc score

tag: overall survival (in days)


title: Rectal biopsy 263

tag: dead (1)/alive(0)


title: R3_D12_amb_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_penn_root_Pool2_LnRep2.fq.gz

value: root


title: Rectal biopsy 256

value: patient with rectal adenocarcinoma

tag: gender


title: R3_D09_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: WT CT32 RNA-Seq rep1

tag: age

value: WT


title: Sample 121: H13_H2

tag: cell type

tag: time point


title: WT CT30 RNA-Seq rep1

tag: genotype/variation


title: R3_D09_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: Rectal biopsy 251


title: Sample 123: H13_H3

tag: subset

tag: chain type

tag: irepertoire barcode


title: Sample 119: H13_H1

value: Immature

tag: health status


title: Rectal biopsy 244

value: Female


title: Rectal biopsy 249


title: Rectal biopsy 226


title: Rectal biopsy 227


title: Sample 118: H12_L4

value: Plasmacyte

value: Light - Kappa and Lambda


title: WT CT28 RNA-Seq rep1

tag: strain

value: C57BJ/L6 background


title: WT CT26 RNA-Seq rep2


title: R3_D09_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_root_Pool2_LnRep4.fq.gz

tag: day

tag: r

tag: lnrep


title: Rectal biopsy 164

tag: subject status


title: Rectal biopsy 163

tag: ajcc score


title: Sample 120: H13_L1

tag: tissue

value: Peripheral blood

value: Healthy


title: R3_D09_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_root_Pool2_LnRep1.fq.gz

tag: pool


title: Rectal biopsy 259

tag: gender

tag: overall survival (in days)

tag: dead (1)/alive(0)


title: WT CT28 RNA-Seq rep2

tag: age


title: R3_D09_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_root_Pool2_LnRep2.fq.gz


title: Sample 116: H12_L3

tag: cell type

value: B cells

value: Memory

tag: time point


title: Sample 114: H12_L2

tag: subset

value: Naïve

tag: chain type


title: WT CT26 RNA-Seq rep1

tag: genotype/variation


title: WT CT24 RNA-Seq rep2

tag: strain


title: WT CT22 RNA-Seq rep2


title: Sample 117: H12_H4

value: Heavy

tag: irepertoire barcode

tag: health status


title: WT CT22 RNA-Seq rep1

value: Male


title: R3_D09_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_root_Pool1_LnRep1.fq.gz

tag: day

tag: r

tag: lnrep


title: Sample 112: H12_L1

tag: tissue


title: R3_D09_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_shoot_Pool2_LnRep4.fq.gz

value: amb

tag: pool

value: shoot


title: WT CT20 RNA-Seq rep2

tag: gender

value: 8-12 weeks of age


title: R3_D09_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_shoot_Pool1_LnRep1.fq.gz

value: ele


title: R3_D09_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: R3_D09_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_penn_root_Pool2_LnRep3.fq.gz

value: root


title: Sample 115: H12_H3


title: WT CT24 RNA-Seq rep1

value: WT


title: Rectal biopsy 107

description: Gene expression in pretreated rectal cancer biopsy measured in frozen tissue

tag: subject status

value: patient with rectal adenocarcinoma

tag: ajcc score

tag: overall survival (in days)


title: Rectal biopsy 112

tag: dead (1)/alive(0)

tag: age


title: Sample 111: H12_H1

tag: cell type

tag: subset

value: Immature

tag: time point


title: Rectal biopsy 135

value: Female


title: Rectal biopsy 150


title: Rectal biopsy 105


title: R3_D09_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: Rectal biopsy 130


title: Rectal biopsy 153


title: WT CT18 RNA-Seq rep2

tag: strain

value: C57BJ/L6 background

tag: genotype/variation


title: R3_D09_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: Sample 110: H11_L4

value: Peripheral blood

value: Plasmacyte

tag: chain type

value: Light - Kappa and Lambda

tag: irepertoire barcode

tag: health status


title: WT CT20 RNA-Seq rep1


title: Sample 109: H11_H4

value: B cells

value: Healthy


title: Sample 108: H11_L3

value: Memory


title: WT CT16 RNA-Seq rep2

value: Male


title: R3_D09_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_shoot_Pool1_LnRep1.fq.gz

value: amb

tag: day

tag: r

tag: lnrep


title: WT CT18 RNA-Seq rep1

tag: gender


title: R3_D09_amb_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_penn_root_Pool2_LnRep4.fq.gz

tag: pool

tag: tissue


title: WT CT16 RNA-Seq rep1